Mr. Bones

Suppose your father is working on a case in his office. He's working on this case for a very long time.
A very, very long time.
A very, very, very, very, very, veryveryveryveryveryveryveryveryveeeeeeeeeeeeeery long time.
He never leaves his office, but you knock on the door every day to say good-morning to him.
One day, he doesn't answer.
You turn the doorknob. The door yields, but on the other side, you see no father. All you see is a pile of old bones and rotten flesh, sitting in your father's favorite chair, its bony fingers curled around your father's favorite mug. Its cracked skull resting on your father's desk, on his open notebook.
The doorknob to the bathroom turns.
The door slowly crrrreeeeaks open...
And in walks your father, entirely unharmed.
He seems completely unsurprised to see the skeleton there. You're glad to see him safe, but as the skeleton starts to rattle, one question remains on your mind.

THEN WHO WAS BONE??!!